Diagnosis of spontaneous bacterial peritonitis and an in situ hybridization approach to detect an "unidentified" pathogen

16S rRNA Next-Generation Sequencing May Not Be Useful for Examining Suspected Cases of Spontaneous Bacterial Peritonitis

Background and Objectives: Ascites, often associated with liver cirrhosis, poses diagnostic challenges, particularly in detecting bacterial infections. Traditional methods have limitations, prompting the exploration of advanced techniques such as 16S rDNA next-generation sequencing (NGS) for improved diagnostics in such low-biomass fluids. The aim of this study was to investigate whether the NGS method enhances detection sensitivity compared to a conventional ascites culture. Additionally, we aimed to explore the presence of a microbiome in the abdominal cavity and determine whether it has a sterile condition. Materials and Methods: Ten patients with clinically suspected spontaneous bacterial peritonitis (SBP) were included in this study. A traditional ascites culture was performed, and all ascites samples were subjected to 16S ribosomal RNA gene amplification and sequencing. 16S rRNA gene sequencing results were interpreted by comparing them to positive and negative controls for each sample. Results: Differential centrifugation was applied to all ascites samples, resulting in very small or no bacterial pellets being harvested. The examination of the 16S amplicon sequencing libraries indicated that the target amplicon products were either minimally visible or exhibited lower intensity than their corresponding negative controls. Contaminants present in the reagents were also identified in the ascites samples. Sequence analysis of the 16S rRNA gene of all samples showed microbial compositions that were akin to those found in the negative controls, without any bacteria isolated that were unique to the samples. Conclusions: The peritoneal cavity and ascites exhibit low bacterial biomass even in the presence of SBP, resulting in a very low positivity rate in 16S rRNA gene sequencing. Hence, the 16S RNA sequencing method does little to enhance the rate of positive samples compared to traditional culture methods, including in SBP cases.

Nosocomial vs healthcare associated vs community acquired spontaneous bacterial peritonitis: Network meta-analysis

INTRODUCTION

Spontaneous bacterial peritonitis (SBP) is a common complication in decompensated liver cirrhosis with ascitic fluid polymorphonuclear cell count > 250/mm3. Community acquired SBP (CA-SBP) occurs within the first 48 hours after hospital admission. Nosocomial SBP (N-SBP) occurs 48-72 hours after hospitalization. Healthcare associated SBP (HA-SBP) occurs in patients hospitalized in the preceding 90 days to months. We aim to evaluate mortality and resistance patterns to third generation cephalosporin among the three types.

METHODS

Multiple databases were systematically searched from inception through August 1st, 2022. Both pairwise (direct) and network (direct + indirect) meta-analysis was performed using a random effects model and DerSimonian Laird approach. Relative Risk (RR) with 95% confidence intervals (CI) were calculated. Network meta-analysis was conducted using frequentist approach.

RESULTS

A total of 14 studies with a total of 2302 SBP episodes were evaluated. On direct meta-analysis, mortality rate was higher in N-SBP compared to HA-SBP (RR 1.84, CI 1.43- 2.37) and CA-SBP (RR 1.69, CI 1.4-1.98), but not significantly different between HA-SBP and CA-SBP (RR=1.40, CI=0.71-2.76). Resistance to third generation cephalosporins was significantly higher in N-SBP compared to HA-SBP (RR=2.02, CI 1.26-3.22) and CA-SBP (RR=3.96, CI=2.50-3.60) as well as in HA-SBP compared to CA-SBP (RR=2.25, CI=1.33-3.81).

CONCLUSIONS

Our network meta-analysis shows increased mortality and antibiotic resistance with nosocomial SBP. We recommend clearly identifying such patients to manage accordingly as well as developing guidelines geared towards nosocomial infections to be able to optimally steer resistance patterns and reduce mortality.

TRAF3 suppression encourages B cell recruitment and prolongs survival of microbiome-intact mice with ovarian cancer

BACKGROUND

Ovarian cancer (OC) is known for exhibiting low response rates to immune checkpoint inhibitors that activate T cells. However, immunotherapies that activate B cells have not yet been extensively explored and may be a potential target, as B cells that secrete immunoglobulins have been associated with better outcomes in OC. Although the secretion of immunoglobulins is often mediated by the microbiome, it is still unclear what role they play in limiting the progression of OC.

METHODS

We conducted an in-vivo CRISPR screen of immunodeficient (NSG) and immune-intact wild type (WT) C57/BL6 mice to identify tumor-derived immune-escape mechanisms in a BRAC1- and TP53-deficient murine ID8 OC cell line (designated ITB1). To confirm gene expression and signaling pathway activation in ITB1 cells, we employed western blot, qPCR, immunofluorescent staining, and flow cytometry. Flow cytometry was also used to identify immune cell populations in the peritoneum of ITB1-bearing mice. To determine the presence of IgA-coated bacteria in the peritoneum of ITB1-bearing mice and the ascites of OC patients, we employed 16S sequencing. Testing for differences was done by using Deseq2 test and two-way ANOVA test. Sequence variants (ASVs) were produced in Qiime2 and analyzed by microeco and phyloseq R packages.

RESULTS

We identified tumor necrosis factor receptor-associated factor 3 (TRAF3) as a tumor-derived immune suppressive mediator in ITB1 cells. Knockout of TRAF3 (TRAF3KO) activated the type-I interferon pathway and increased MHC-I expression. TRAF3KO tumors exhibited a growth delay in WT mice vs. NSG mice, which was correlated with increased B cell infiltration and activation compared to ITB1 tumors. B cells were found to be involved in the progression of TRAF3KO tumors, and B-cell surface-bound and secreted IgA levels were significantly higher in the ascites of TRAF3KO tumors compared to ITB1. The presence of commensal microbiota was necessary for B-cell activation and for delaying the progression of TRAF3KO tumors in WT mice. Lastly, we observed unique profiles of IgA-coated bacteria in the ascites of OC-bearing mice or the ascites of OC patients.

CONCLUSIONS

TRAF3 is a tumor-derived immune-suppressive modulator that influences B-cell infiltration and activation, making it a potential target for enhancing anti-tumor B-cell responses in OC.

Rapid and Simple Approaches for Diagnosis of Staphylococcus aureus in Bloodstream Infections

Staphylococcus aureus is an important causative pathogen of bloodstream infections. An amplification assay such as real-time PCR is a sensitive, specific technique to detect S. aureus. However, it needs well-trained personnel, and costs are high. A literature review focusing on rapid and simple methods for diagnosing S. aureus was performed. The following methods were included: (a) Hybrisep in situ hybridization test, (b) T2Dx system, (c) BinaxNow Staphylococcus aureus and PBP2a, (d) Gram staining, (e) PNA FISH and QuickFISH, (f) Accelerate Pheno^TM system, (g) MALDI-TOF MS, (h) BioFire FilmArray, (i) Xpert MRSA/SA. These rapid and simple methods can rapidly identify S. aureus in positive blood cultures or direct blood samples. Furthermore, BioFire FilmArray and Xpert MRSA/SA identify methicillin-resistant S. aureus (MRSA), and the Accelerate Pheno^TM system can also provide antimicrobial susceptibility testing (AST) results. The rapidity and simplicity of results generated by these methods have the potential to improve patient outcomes and aid in the prevention of the emergence and transmission of MRSA.

Therapeutic Drug Monitoring of Amphotericin-B in Plasma and Peritoneal Fluid of Pediatric Patients after Liver Transplantation: A Case Series

Fungal infections represent a serious complication during the post-liver transplantation period. Abdominal infections can occur following pre-existing colonization, surgical procedures, and permanence of abdominal tubes. In our center, liposomal amphotericin-B is used as antifungal prophylaxis in pediatric patients undergoing liver transplantation. The aim of this study is to evaluate peritoneal levels of amphotericin-B following intravenous administration. Six liver recipients received liposomal amphotericin-B. Three of them were treated as prophylaxis; meanwhile, three patients received liposomal amphotericin-B to treat Candida albicans infection. Plasma and peritoneal amphotericin-B levels were measured by LC-MS/MS in two consecutive samplings. Cmin (pre-dose) and Cmax (2 h after the end of infusion) were evaluated as drug exposure parameters for both plasma and peritoneum. Our results showed that peritoneal amphotericin-B levels were significantly lower than plasma and that the correlation coefficient was 0.72 (p = 0.03) between plasma and peritoneal Cmin. Moreover, although peritoneal levels were within the therapeutic range, they never reached the PK/PD target (Cmax/MIC > 4.5). In conclusion, PK exposure parameters could be differently used to analyze amphotericin-B concentrations in plasma and peritoneum. However, liposomal amphotericin-B should be preferred in these patients as prophylactic rather than therapeutic treatment for fungal infections.

Ascitic Calprotectin as an early predictor of hepatocellular carcinoma in patients with cirrhotic ascites

BACKGROUND

Calprotectin is a heterodimer formed by S100A8 and S100A9 proteins which are enhanced during hepatic carcinogenesis and the increased expression of both proteins promotes malignant progression of hepatocellular carcinoma. The potential correlation between ascitic Calprotectin and HCC was not studied.

METHODS

100 patients were stratified into a case group which enrolled 50 patients with cirrhotic ascites and documented HCC and a control group consisted of 50 patients with cirrhotic ascites without HCC. They were evaluated by liver function tests, abdominal ultrasound and routine ascitic fluid examination including ascetic Calprotectin and results were validated in another group (n = 100).

RESULTS

Calprotectin level was significantly higher in the HCC group with insignificant difference regarding total cell count, PNLs, ascitic albumin, LDH, CEA and SAAG. It correlated with serum creatinine (r = 0.245, p = 0.014) and number of focal hepatic lesions (r = 0.309, p = 0.002). In the validation group, 28 patients had elevated ascitic Calprotectin of which 21 patients had developed HCC (75%) after a mean period of 3.8 ± 1.54 months. A cut of value 126 ng/ml was accurate to predict HCC in liver cirrhosis with ascites with a sensitivity of 93.3% specificity 94%, AUC 0.950, Youden's J value = 0.873, p = 0.0001.

CONCLUSION

Ascitic Calprotectin may offer an easy, affordable marker that can predict the early occurrence of HCC.

Emerging Gram-positive bacteria and drug resistance in cirrhosis patients with spontaneous bacterial peritonitis: A retrospective study

Spontaneous bacterial peritonitis (SBP) is one of the most severe complications in liver cirrhosis (LC) patients with ascites. The aim of the present study was to retrospectively analyze the bacterial spectrum and drug resistance in ascites culture of patients with SBP. A total of 3, 189 patients with ascites were enrolled in the present study, including 912 LC patients, of which 247 had SBP. It was revealed that in the 3, 189 patients, the ratio of SBP exhibited annual increases, especially in 2015, and this trend remained when cases were divided into two groups: Group A (admission, 2011-2013) and Group B (admission, 2014-2016). The 247 SBP patients were then stratified into two groups: Group 1 (admission, 2011-2013) and Group 2 (admission, 2014-2016). The rate of infection with gram-positive bacteria (GPB) was markedly higher in Group 2 compared with Group 1. Over time, GPB and gram-negative bacteria (GNB) were increased, while the increase of GPB was greater than that of GNB. Direct bilirubin and C-reactive protein levels, and the positive rate of ascites culture in Group 2 were greater than in Group 1. Furthermore, marked differences in serological and ascitic indexes or pathogeny, as well as complications between the patients with GPB and GNB infection were observed. The results regarding drug sensitivity revealed that the resistance rate of GPB and GNB to penicillin (ampicillin) was 100%, while the resistance rate to amikacin, imipenem, meropenem and piperacillin/tazobactam was 0% for GNB, and similarly, the resistance rate to vancomycin, teicoplanin, amikacin and linezolid was 0% for GPB. The results suggested that combined use of ampicillin/sulbactam or piperacillin/tazobactam should be selected forempirical therapy. In cases of nosocomial infection, these drugs should be combined with vancomycin, linezolid or teicoplanin when required.

Treatment for cirrhotic ascites

Common complications of decompensated liver cirrhosis are esophageal varices, hepatic encephalopathy and ascites. After the onset of complications, the prognosis worsens. In patients with ascites, the 5-year mortality rate is 44%. Furthermore, hyponatremia, spontaneous bacterial translocation and hepatorenal syndrome also greatly worsen the prognosis. Effective treatment of cirrhotic ascites improves the quality of life and survival rate. Recently, the newly produced diuretic, tolvaptan (vasopressin V2 receptor antagonist), was reported to be effective in the treatment of refractory ascites in liver cirrhosis; however, there has not been an associated positive effect on the prognosis. There are various types of treatment for ascites, such as large-volume paracenteses, a cell-free and concentrated ascites reinfusion therapy, a transjugular intrahepatic portosystemic shunt, and a peritoneo-venous shunt. Although they improve the prognosis, liver transplantation remains the ultimate form of treatment. The present article discusses the therapeutic management of cirrhotic ascites.

Combinational approach using in situ hybridization targeting 23S ribosomal RNA genes and blood cultures for bacterial identification in patients with neutropenia and fever

BACKGROUND

A new 23S ribosomal RNA genes-targeted in situ hybridization (ISH) probe to detect global bacterial genomic DNA (59 species from 35 genera; referred to as the GB probe) phagocytized in leukocytes was recently developed. This method provided early and direct evidence of bacterial infection with high sensitivity and specificity in spontaneous bacterial peritonitis ascites. However, the utility of this method in febrile neutropenia (FN) is unknown.

METHODS

We prospectively evaluated the utility of the ISH approach using the GB probe and previously reported probes in patients with neutropenia and fever undergoing chemotherapy at our institution between June 2011 and July 2013. Blood samples for culture analysis and ISH tests were collected simultaneously at the onset of fever; the latter were performed repeatedly.

RESULTS

Fifty febrile episodes were evaluated. In 24 episodes of fever of unknown origin and 15 episodes of local infection (all negative for blood cultures), ISH tests identified causal bacteria in 21% and 13% of cases, respectively, at the onset of fever. In seven sepsis cases (all positive for blood culture), positive ISH test results at fever onset were achieved in 71%; for two patients with neutrophil counts of 0/μl and 171/μl, respectively, negative results were obtained.

CONCLUSIONS

This new ISH approach could prove useful for early detection of bacteria in patients with neutropenia and blood culture-negative, with fever of unknown etiology after chemotherapy. Using this method in combination with blood culture, even in cases with extremely low neutrophil counts, might contribute to better management of FN.

Impact of hepatic function on serum procalcitonin for the diagnosis of bacterial infections in patients with chronic liver disease: A retrospective analysis of 324 cases

Although procalcitonin (PCT) is a valid marker for early diagnosis of bacterial infections, it is unclear whether its accuracy in predicting bacterial infections is affected by impaired liver function. This study aimed to assess the impact of compromised liver function on the diagnostic value of PCT.This retrospective study was conducted between January 2013 and May 2015. A total of 324 patients with chronic liver disease were enrolled. Routine laboratory measurements and PCT were performed. Patients were divided into 3 groups according to clinical diagnosis: chronic hepatitis (group 1), decompensated cirrhosis (group 2), and acute-on-chronic liver failure/chronic liver failure (group 3). The correlation between PCT and liver function was analyzed. The area under the receiver operating characteristic (AUCROC) curve of PCT was analyzed according to infection status and liver function.PCT was more accurate than white blood cell count (P < 0.001) and percentage of neutrophils (P < 0.001) in detecting bacterial infections in patients with impaired liver function. In patients without infection, PCT had a moderate positive correlation with serum total bilirubin (TBIL) (r = 0.592), and a weak correlation with model for end-stage liver disease score (r = 0.483) and international normalized ratio (r = 0.389). The AUCROC and optimum thresholds of PCT and for predicting bacterial infections at different levels of TBIL were 0.907 (95% CI 0.828-0.958) and 0.38 ng/mL, respectively, for TBIL <5 mg/dL, 0.927 (95% CI 0.844-0.974) and 0.54 ng/mL (5 mg/dL ≤TBIL<10 mg/dL), 0.914 (95% CI 0.820-0.968) and 0.61 ng/mL (10 mg/dL ≤TBIL<20 mg/dL), 0.906 (95% CI 0.826-0.958) and 0.94 ng/mL (TBIL ≥20 mg/dL), respectively.This study demonstrated that PCT was a valuable marker of bacterial infection in patients with chronic liver diseases. TBIL affected PCT threshold, so different cut-offs should be used according to different TBIL values.

An optimized staining technique for the detection of Gram positive and Gram negative bacteria within tissue

BACKGROUND

Bacterial infections are a common clinical problem in both acute and chronic wounds. With growing concerns over antibiotic resistance, treatment of bacterial infections should only occur after positive diagnosis. Currently, diagnosis is delayed due to lengthy culturing methods which may also fail to identify the presence of bacteria. While newer costly bacterial identification methods are being explored, a simple and inexpensive diagnostic tool would aid in immediate and accurate treatments for bacterial infections. Histologically, hematoxylin and eosin (H&E) and Gram stains have been employed, but are far from optimal when analyzing tissue samples due to non-specific staining. The goal of the current study was to develop a modification of the Gram stain that enhances the contrast between bacteria and host tissue.

FINDINGS

A modified Gram stain was developed and tested as an alternative to Gram stain that improves the contrast between Gram positive bacteria, Gram negative bacteria and host tissue. Initially, clinically relevant strains of Pseudomonas aeruginosa and Staphylococcus aureus were visualized in vitro and in biopsies of infected, porcine burns using routine Gram stain, and immunohistochemistry techniques involving bacterial strain-specific fluorescent antibodies as validation tools. H&E and Gram stain of serial biopsy sections were then compared to a modification of the Gram stain incorporating a counterstain that highlights collagen found in tissue. The modified Gram stain clearly identified both Gram positive and Gram negative bacteria, and when compared to H&E or Gram stain alone provided excellent contrast between bacteria and non-viable burn eschar. Moreover, when applied to surgical biopsies from patients that underwent burn debridement this technique was able to clearly detect bacterial morphology within host tissue.

CONCLUSIONS

We describe a modification of the Gram stain that provides improved contrast of Gram positive and Gram negative microorganisms within host tissue. The samples used in this study demonstrate that this staining technique has laboratory and clinical applicability. This modification only adds minutes to traditional Gram stain with reusable reagents, and results in a cost- and time-efficient technique for identifying bacteria in any clinical biopsy containing connective tissue.

A quick screening model for symptomatic bacterascites in cirrhosis

BACKGROUND

Diagnosis of spontaneous bacterial peritonitis in cirrhosis can be made when a patient has an ascites polymorphonuclear leukocyte count ≥250/mm3. However, symptomatic bacterascites, which is a variant of spontaneous bacterial peritonitis with signs of infection but an ascites polymorphonuclear leukocyte count <250/mm3, cannot be confirmed until the time-consuming ascites culture becomes positive. Currently, early indicators for symptomatic bacterascites remain undetermined.

AIMS

To develop a quick screening model for early detection of symptomatic bacterascites in cirrhosis.

MATERIALS AND METHODS

Data on patients with cirrhotic ascites from two hospitals (from 2010 to 2014) were collected retrospectively. Patients with symptomatic bacterascites were enrolled in the case group and compared with patients without any infection in the control group. Logistic regression analysis was used to build a model for screening symptomatic bacterascites, and a receiver operating characteristics curve was used to assess the model.

RESULTS

In total, 103 patients were enrolled in the case group and 204 patients were enrolled in the control group. A screening model was constructed based on body temperature, abdominal tenderness, blood neutrophil percentage, blood total bilirubin, prothrombin time, and ascites nucleated leukocyte count. The area under the receiver operating characteristic curve was 0.939; a screening score of 0.328 was the best cutoff value.

CONCLUSION

Patients with suspected symptomatic bacterascites can be quickly screened according to the developed model, and a screening score ≥0.328 indicates symptomatic bacterascites.